Using community_rrna with Silva reference database for taxonomy about miceco

[Russel88]

Hi,

Yes, the OTU-table should have samples as columns and the frequency of them. This function was written back when Greengenes wasn't so outdated. I would suggest that you align your OTUs against the rrnDB database. This way you can obtain a data.frame with the estimated copy number for each OTU: https://rrndb.umms.med.umich.edu/

Cheers,
Jakob

[bippuspm]

Jakob, That's exactly what I did--thank you! My only concern is I got a warning that said "the condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be used". Does this warning mean it wasn't able to be weighted by abundances? Thanks, Paige

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-- Paige Varner PhD Candidate Civil and Environmental Engineering I Duke University Contact: ***@***.*** | she/her

________________________________ From: Jakob Russel ***@***.***> Sent: Friday, September 2, 2022 2:32 PM To: Russel88/MicEco ***@***.***> Cc: Paige Varner ***@***.***>; Author ***@***.***> Subject: Re: [Russel88/MicEco] Using community_rrna with Silva reference database for taxonomy (Issue #19) Hi, Yes, the OTU-table should have samples as columns and the frequency of them. This function was written back when Greengenes wasn't so outdated. I would suggest that you align your OTUs against the rrnDB database. This way you can obtain a data.frame with the estimated copy number for each OTU: https://rrndb.umms.med.umich.edu/<https://urldefense.com/v3/__https://rrndb.umms.med.umich.edu/__;!!OToaGQ!rnZP5P0MiRE0FdSPqwc_u1VOTInQsiFBn61a_yEQV1At5ZsWHeg4w0HsV6-DiMsoSpXLrSHhb_kZIn86HJlQTEWhtdoR$> Cheers, Jakob — Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https://github.com/Russel88/MicEco/issues/19*issuecomment-1235796609__;Iw!!OToaGQ!rnZP5P0MiRE0FdSPqwc_u1VOTInQsiFBn61a_yEQV1At5ZsWHeg4w0HsV6-DiMsoSpXLrSHhb_kZIn86HJlQTF98V4FM$>, or unsubscribe<https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AKDLSIHBDBXSUVKFJRKPYPTV4JB3VANCNFSM6AAAAAAQDI6PUM__;!!OToaGQ!rnZP5P0MiRE0FdSPqwc_u1VOTInQsiFBn61a_yEQV1At5ZsWHeg4w0HsV6-DiMsoSpXLrSHhb_kZIn86HJlQTLOORL2_$>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[Russel88]

Hi Paige,

Could you send the code you used and the full error message. It's hard to say what has gone wrong from what you write.

[Russel88]

Closing due to no answer